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Status |
Public on Nov 30, 2014 |
Title |
VestibularSchwannoma_NF2_5 |
Sample type |
genomic |
|
|
Source name |
Vestibular Schwannoma (NF2)
|
Organism |
Homo sapiens |
Characteristics |
cell type: Vestibular Schwannoma tissue type: Tumor subtype: NF2 associated
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was isolated using the Wizard Genomic DNA purification kit (Promega), according to the manufacturer’s instructions. Bisulfite-treated using the EZ DNA methylation Kit (Zymo Research, Orange, CA, USA), according to the manufacturer’s instructions.
|
Label |
Cy5 and Cy3
|
Label protocol |
Standard Illumina Protocol
|
|
|
Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip, using standard Illumina protocols.
|
Scan protocol |
Arrays were scanned using BeadArray Reader by standard recommended Illumina scanner settings
|
Description |
Neurofibromatosis 2 patient
|
Data processing |
M-value was obtained with lumi R package after background correction, color bias adjustment by quantiles and SSN normalization ProcessedMatrix.txt: Avg_Beta correspond to M-value after processing with lumi package: Barckground correction, color bias adjustment and normalization by ssn. p_value were obtained with GenomeStudio. This table is prepared for using in IMA package. Rawdata.txt: Value outputed by lumi package after direct import from iDAT files. Was done using importMethyIDAT function, which give this non-processed value.
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|
|
Submission date |
Apr 08, 2014 |
Last update date |
Nov 30, 2014 |
Contact name |
Miguel Torres-Martin |
E-mail(s) |
migtorres.martin@gmail.com
|
Organization name |
Hospital Universitari Germans Trias i Pujol
|
Department |
Clinical Genomics Unit
|
Street address |
Carretera de Canyet, s/n
|
City |
Badalona |
State/province |
Barcelona |
ZIP/Postal code |
08916 |
Country |
Spain |
|
|
Platform ID |
GPL13534 |
Series (2) |
GSE56596 |
Wide methylation analysis in vestibular schwannoma [Infinium HumanMethylation450 BeadChip] |
GSE56598 |
Wide methylation analysis in vestibular schwannoma |
|